[Halfjack]

We haven't yet delved into a lot of company play yet, but by the book the company dice aren't explicitly allocated, so I'd guess whichever player takes the reins rolls the dice. As for obstacles, certainly the most interesting obstacles are going to be other companies -- expanding your territory at the expense of the desert nomads, undermining the sovereignty of the pirate king in order to win away skilled pilots, and so on. There's no particular reason why more passive elements can't be obstacles set by the GM rather than opposed by a company, though -- say attempting to colonise some particularly rugged area or cross a famously treacherous sea path in order to establish more lucrative trade. To go a little further, there are even some monsters that are better represented at company scale than character scale, allowing you to pit your kingdom against a vast demon threat, for example.

In the end, the company mechanics benefit from the parallel with character mechanics insofar as the resolution system is essentially identical and is generalised enough that it scales to the company scope effectively. The only real change in the game mechanics at the scale is to set a time scale of a month per roll for companies and to allow character activity when zoomed in to modify the company scale dice rolls positively or negatively depending on the character scale success.